Contacts of the strand formed by residues 154 - 163 (chain F) in PDB entry 1N13
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 154 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E SER 3.3 8.7 - - - -
26E GLU* 3.6 12.4 + - - -
33E ALA* 4.5 1.8 - - - -
81F ILE* 3.2 6.8 - - - +
82F SER 2.9 34.2 + - - -
89F ILE* 3.5 8.2 - - - +
148F HIS* 3.8 8.3 - - - -
150F VAL* 4.0 3.5 - - - +
153F LEU* 1.3 75.8 - - - +
155F CYS* 1.3 61.3 + - - -
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Residues in contact with CYS 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E SER* 3.0 27.3 - - - -
25E SER 2.9 9.2 + - - -
33E ALA* 3.8 22.9 - - + +
34E PHE* 3.9 25.1 - - - -
37E ALA* 3.8 16.6 - - - +
79F TYR* 4.4 2.9 - - - -
80F ILE 3.2 9.2 - - - -
81F ILE* 3.8 18.2 - - + -
89F ILE* 4.1 2.4 - - - +
148F HIS* 4.3 2.0 - - - -
154F GLY* 1.3 74.8 - - - +
156F ALA* 1.3 71.5 + - - +
157F PHE* 4.4 1.8 - - - -
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Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY 3.8 4.0 - - - -
24E SER* 4.2 2.0 - - - -
79F TYR* 3.1 7.3 - - - +
80F ILE* 3.0 37.1 + - + -
89F ILE* 3.8 27.5 - - + +
90F SER* 3.9 19.5 - - - -
91F ALA* 3.6 4.3 - - + +
146F VAL* 4.3 7.6 - - + +
148F HIS* 4.4 5.2 - - + -
155F CYS* 1.3 72.3 - - - +
157F PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 4.4 0.7 - - + -
22E ALA* 3.1 2.3 - - - -
23E GLY 2.8 41.8 + - - +
34E PHE* 4.0 12.3 - + - -
37E ALA* 3.9 15.5 - - + -
38E LEU* 3.4 33.0 - - + -
41E ALA* 4.0 20.0 - - + -
43E ILE* 4.1 16.4 - - + -
48E LEU* 4.0 15.7 - - + -
77F TYR* 3.6 26.9 - + + -
78F GLY 3.5 9.9 - - - -
79F TYR* 4.1 2.7 - - + -
91F ALA* 3.8 3.5 - - - +
146F VAL* 3.3 5.3 - - - +
155F CYS* 4.4 4.3 - - - -
156F ALA* 1.3 75.6 - - - +
158F ALA* 1.3 63.3 + - - +
159F ALA* 3.4 30.5 - - + -
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Residues in contact with ALA 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL 3.4 9.0 - - - +
22E ALA* 4.2 6.3 - - + -
77F TYR* 3.3 3.9 - - - +
78F GLY 3.0 32.7 + - - +
91F ALA* 3.7 6.0 - - + +
92F ALA* 3.6 42.2 - - - +
93F ILE* 3.3 7.6 - - + +
144F ILE* 4.5 2.9 - - + -
157F PHE* 1.3 76.9 - - - +
159F ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E SER 3.6 0.3 - - - +
20E LEU* 3.3 6.2 - - - +
21E VAL* 2.7 45.5 + - + +
43E ILE* 5.7 0.9 - - + -
75F THR* 3.6 14.6 - - + -
76F ALA 3.2 11.9 - - - +
77F TYR* 3.7 0.9 - - + -
93F ILE* 3.5 9.1 - - - +
157F PHE* 3.4 27.8 - - + -
158F ALA* 1.3 76.3 - - - +
160F ALA* 1.3 61.2 + - - +
161F ALA 4.0 0.7 - - - -
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Residues in contact with ALA 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL* 4.0 6.7 - - + -
19E SER 3.3 6.5 - - - -
20E LEU* 3.8 16.6 - - + -
51E ILE* 4.9 2.4 - - - +
75F THR* 3.4 3.1 - - - -
76F ALA* 2.8 31.6 + - - +
93F ILE* 3.9 2.7 - - + +
107F ILE* 3.7 41.5 - - + -
159F ALA* 1.3 73.8 - - - +
161F ALA* 1.3 61.4 + - - +
162F LEU* 3.8 1.8 + - - +
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Residues in contact with ALA 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E THR 4.4 0.2 - - - -
18E VAL* 3.4 3.5 - - - -
19E SER* 2.8 38.2 + - - +
21E VAL* 5.5 2.9 - - + -
43E ILE* 3.9 28.0 - - + -
64F LEU* 4.2 15.0 - - + -
73F VAL* 3.9 13.0 - - + -
74F PRO 3.8 4.3 - - - -
75F THR* 4.1 4.9 - - + +
159F ALA 4.0 0.6 - - - -
160F ALA* 1.3 71.6 - - - +
162F LEU* 1.3 62.5 + - - +
163F TRP* 3.7 3.9 + - + +
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Residues in contact with LEU 162 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASN* 3.8 14.1 - - - +
72B LEU* 4.5 1.8 - - + -
15E PRO* 3.7 23.3 - - + +
17E THR 3.3 4.7 - - - +
18E VAL* 3.9 28.0 - - + -
51E ILE* 3.9 18.4 - - + -
54F ILE 3.8 17.5 - - - +
55F MET* 4.5 1.1 - - - -
56F PRO* 4.1 21.8 - - + -
73F VAL* 3.7 2.8 - - - +
74F PRO* 2.9 44.4 + - + +
107F ILE* 4.3 11.7 - - + -
160F ALA 4.9 1.3 - - - +
161F ALA* 1.3 71.8 - - - +
163F TRP* 1.3 65.4 + - - +
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Residues in contact with TRP 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 6.0 0.7 - - + -
3E ALA 5.9 2.5 - - - -
5E ILE* 4.2 24.0 - - + -
7E PRO* 5.1 0.2 - - + -
15E PRO* 3.3 4.0 - - - +
16E ASN 2.9 24.6 + - - -
17E THR* 2.9 23.2 + - - +
19E SER* 5.8 1.1 - - - +
64F LEU* 6.3 0.9 - - + -
65F PRO* 4.2 20.1 - - + +
66F LYS 5.1 2.4 + - - -
67F LEU* 3.6 26.9 - - + +
68F PRO* 4.1 22.2 - - + +
71F ALA* 3.9 18.2 - - + -
72F LEU 3.6 22.7 - - - -
73F VAL* 3.9 18.2 - - + -
74F PRO* 4.6 1.3 - - + -
161F ALA* 3.7 4.6 + - + +
162F LEU* 1.3 83.1 - - - +
164F TYR* 1.3 105.1 + + + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il